Role of Genetic Analysis for the Differential Diagnosis of Delayed Puberty from the UK Puberty Cohort

Abstract

Abstract Distinction between self-limited delayed puberty (DP) and idiopathic hypogonadotropic hypogonadism (IHH) is challenging. Several biochemical tests have been applied to differentiate these conditions; however, all have limitations resulting in some patients undergoing inappropriate investigations and treatment. This study investigated whether the identification of a genetic defect in patients presenting with pubertal delay in adolescence through whole exome sequencing (WES) can help in distinguishing these two conditions. The WES data of 47 pubertal delay patients from Paediatric Endocrinology and Paediatric services around the UK were analysed. The variants were filtered for rare, predicted deleterious variants in genes from a virtual panel reported in IHH (n= 36), both IHH and self-limited (n=6), and self-limited DP (n= 4) that segregated with trait. Pathogenic variants were verified by Sanger sequencing, computational bioinformatics, and review of inheritance pattern as compared to previous reported mutations in this gene, and assigned a genotypic diagnosis as self-limited DP, IHH or overlapping. Full clinical history, physical examination and basic laboratory and hormonal investigations were used to determine the clinical diagnosis. Clinically, 38% of patients had self-limited DP and 26% had IHH and the rest of uncertain diagnosis as they were still undergoing a period of follow up under the age of 18 years. Twenty-four variants in 17 genes, accounting for 43% of the tested cohort, were identified to be potentially pathogenic variants, with most inherited in a heterozygous manner. We found a good correlation between genotypic diagnosis and phenotype diagnosis with Cohen’s kappa (k) = 0.235 (95% IC, 0.031 to 0.429). Thus, patients who carry variants reported only in self-limited DP with heterozygous inheritance were likely to have a clinical diagnosis of definite self-limited DP. On the other hand, patients carrying homozygous or loss of function variants in genes reported with heterozygous mutations in IHH will be very likely to have IHH. In addition, we identified variants in patients with clinical self-limited DP to have variants, which had been previously reported only in IHH, including DMXL2, CHD7, OTUD4, and SEMA3E. In summary, this study shows that there is a good genotype-phenotype correlation in patients presenting with pubertal delay. Therefore, genetic investigation may help to distinguish these two conditions, resulting in more accurate diagnosis and appropriate treatment modalities. In addition, new genes, previously implicated only in IHH, have been identified in self-limited DP, which indicate that these two conditions share similar disease mechanisms.